I heartily endorse Susan's recommendation that we standardize mutant gene
nomenclature. However, the upper case/lower case distinction that was
established many years ago for yeast has, in my view, is too much of a
simplification to make it informative for modern genetics. The theory is
that it distinguishes between "domant" and "recessive" alleles and that this
distinction is evident in the name. Therein lies the problem.
Dominance is always judged in a vis-a-vis manner and then only by
considering a limited aspect of the phenotype. One pair of alleles may
appear to have one dominance relationship for one aspect of their phenotype
and another for a different - the classical example of cicle cell anemia
comes to mind. As we look more and more into the molecular phenotypes of
mutant genes, this aspect of the problem becomes more acute. In addition,
multiple alleles may be arranged in dominance cascades or in one arrangement
in one genetic background and in another in a different one. This latter
property of genotype-dependent shifts in dominance (read "inter-genic
suppression" or "syntheitc lethal" or whatever your favorite paradigm for
studying gene-gene interactions) is a vital aspect of modern genetic
analysis. For all of these reasons, incorporating a notion of dominance
into the name of a specific allele suggests a fixity of properties that is
It also seems to me to be unhelpful to use upper case names for "wild type"
alleles. Unless we standardize on a single wild type strain, the wild types
that we use will be found to vary from one another. What, then, do we do
about naming the different alleles from the various strains? Hopefully the
strains will not often vary dramatically in their characteristics, but when
they do, the arbitrary identification of wild type alleles as upper case
will not work.
To correctly interpret the meaning of the suggested upper case vs. lower
case distinction, a reader would have do know as much about the various
alleles as if that distinction in naming were not present.
I recommend that we use all lower case letters in the names of all alleles.
I also recommend that we adhere to the present naming conventions for
nuclear genes that code for components of the chloroplast.
mets at cells.uchicago.edu